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Fig. 4 in Algal genomics perspective: the pangenome concept beyond traditional molecular phylogeny and taxonomy

Fig. 4. The pangenome concept based on a comparison of gene inventory. Colored squares indicate commonly shared or newly acquired genes between species or populations.

Fig. 1 in Algal genomics perspective: the pangenome concept beyond traditional molecular phylogeny and taxonomy

Fig. 1. Phase-contrast microscopy images of diverse algal taxa. A. Rhodella maculata CCMP736 (Rhodophyta). B. Dixoniella grisea CCMP1916 (Rhodophyta). C. Emiliania huxleyi (Haptophyta). D. Diacronema lutheri LIMS-PS-0073 (Haptophyta). E. Proteomonas sulcata (Cryptophyta). F. Rhinomonas nottbecki (Cryptophyta). G. Coolia monotis (Alveolata). H. Sungminbooa australiensis (Pelagophyceae; Stramenopiles). I. Halamphora pseudohyalina (Bacillariophyceae; Stramenopiles). J. Navicula avium (Bacillariophyceae; Stramenopiles). K. Thalassiosira gravida (= T. rotula; Bacillariophyceae; Stramenopiles). L. Ditylum sol (Bacillariophyceae; Stramenopiles). Multifocus light microscopy images were merged, and white balances were properly adjusted by Adobe Photoshop and Illustrator (scale bars: A-F, and H-J = 15 μm; G, and K = 40 μm; L = 100 μm).

Fig. 3 in Algal genomics perspective: the pangenome concept beyond traditional molecular phylogeny and taxonomy

Fig. 3. Major photosynthetic algal lineages in the eukaryote Tree of Life (eToL). The eToL is reconstructed based on previous studies (Burki et al., 2019; Keeling and Burki, 2019; Strassert et al., 2019; Bhattacharya and Price, 2020; Sibbald and Archibald, 2020).

Fig. 2. The red algal phylogenomic approaches. A. Concatenated multigene phylogeny using 170 in Algal genomics perspective: the pangenome concept beyond traditional molecular phylogeny and taxonomy

Fig. 2. The red algal phylogenomic approaches. A. Concatenated multigene phylogeny using 170 plastid genes (Muñoz-Gómez et al., 2017). B. Concatenated multigene phylogeny using 4,777 nuclear genes (Lee et al., 2019). C. Intertwining phylogenetic network tree of red algal plastid and nuclear multigene phylogenies.

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Fig. 1 in Taxonomic review of the umbelliferous taxa Heracleum moellendorffii complex in Korea based on molecular phylogenies of nuclear ribosomal ITS sequences

Fig. 1. Cladograms inferred from the analysis of 29 nuclear ribosomal DNA ITS1 and ITS2 sequences from the genus Heracleum and an outgroup. (A) The strict consensus of two minimal length 138-step trees derived from equally weighted maximum parsimony analysis of combined nuclear rDNA ITS and 5.8S sequences (CI's with and without uninformative characters=0.91 and 0.89, respectively; RI=0.95). Numbers above nodes indicate the number of times a monophyletic group occurred in 100 bootstrap replicates; decay values are presented below. (B) The Maximum likelihood tree using a transition/tranversion rate ratio of 1.5. Branch lengths are proportional to the number of expected nucleotide substitutions per site. Boxes A, B, and C indicate clades H. maximum-moellendorffii, H. subbipinnatum, and H. sphondylium, respectively.

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Fig. 3 in Molecular phylogeny provides new insights on the taxonomy and composition of Lyperosomum Looss, 1899 (Digenea, Dicrocoeliidae) and related genera

Fig. 3. Representatives of Lyperosomum petiolatum from different hosts: a – Pica pica; b – Garrulus glandarius; c – Corvus frugilegus; d – Corvus frugilegus, subadult specimen; e, f – Sylvia atricapilla. Lyperosomum sp., from Turdus merula: g – specimen fixed after death; h – specimen fixed under pressure. Scale bars – 1 mm.

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Fig. 1 in Size does not matter: molecular phylogeny reveals one of the largest trematodes from vertebrates, the enigmatic Ithyoclinostomum dimorphum, as a species of Clinostomum (Trematoda: Clinostomidae)

Fig. 1. Metacercariae of Clinostomum dimorphum found in the erythrinid fish, Hoplias intermedius from Brazil: (A) Whole view of a paragenophore specimen. B) Detail of reproductive structures of a hologenophore specimen.

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Fig. 2 in Size does not matter: molecular phylogeny reveals one of the largest trematodes from vertebrates, the enigmatic Ithyoclinostomum dimorphum, as a species of Clinostomum (Trematoda: Clinostomidae)

Fig. 2. Maximum likelihood phylogram based on the concatenated ITS1-5.8S-ITS2 + 28S + cox1 datasets of Clinostomum dimorphum (in bold) and selected species of the family Clinostomidae. Clade formed by isolates of 'Ithyoclinostomum' yamagutii (incertae sedis) is highlighted in grey. Taxon names are followed by GenBank accession numbers of ITS, 28S, and cox1, respectively, and country of record. Branch length scale bar indicates number of substitutions per site. Abbreviations: HON, Honduras; ITA, Italy; KEN, Kenya; MEX, Mexico; THAI, Thailand; USA, United States of America.

Fig. 5 in Morphology, molecular characterization and phylogeny of Bolbosoma nipponicum Yamaguti, 1939 (Acanthocephala: Polymorphidae), a potential zoonotic parasite of human acanthocephaliasis

Fig. 5. Phylogenetic relationships of representatives of the family Polymorphidae using Bayesian inference based on the 18S + ITS +28S + cox1 sequence data. Centrorhynchus clitorideus (Polymorphida: Centrorhynchidae) was chosen as outgroup. Bayesian posterior probabilities values> 0.70 are shown in the phylogenetic tree.

Fig. 4 in Morphology, molecular characterization and phylogeny of Bolbosoma nipponicum Yamaguti, 1939 (Acanthocephala: Polymorphidae), a potential zoonotic parasite of human acanthocephaliasis

Fig. 4. Phylogenetic relationships of representatives of the family Polymorphidae using maximum likelihood method based on the 18S + ITS +28S + cox1 sequence data. Centrorhynchus clitorideus (Polymorphida: Centrorhynchidae) was chosen as outgroup. Bootstrap values> 50 are shown in the phylogenetic tree.

Fig. 3 in Morphology, molecular characterization and phylogeny of Bolbosoma nipponicum Yamaguti, 1939 (Acanthocephala: Polymorphidae), a potential zoonotic parasite of human acanthocephaliasis

Fig. 3. Scanning electron micrographs of Bolbosoma nipponicum collected from Callorhinus ursinus (Linnaeus) (Carnivora: Otariidae) in St. Paul Island, Alaska. A: anterior part of male; B: trunk spines; C: proboscis; D: hooks.

Fig. 2 in Morphology, molecular characterization and phylogeny of Bolbosoma nipponicum Yamaguti, 1939 (Acanthocephala: Polymorphidae), a potential zoonotic parasite of human acanthocephaliasis

Fig. 2. Photomicrographs of Bolbosoma nipponicum collected from Callorhinus ursinus (Linnaeus) (Carnivora: Otariidae) in St. Paul Island, Alaska. A: anterior part of male; B: proboscis; C: posterior part of male; D: posterior part of female.

Fig. 1 in Morphology, molecular characterization and phylogeny of Bolbosoma nipponicum Yamaguti, 1939 (Acanthocephala: Polymorphidae), a potential zoonotic parasite of human acanthocephaliasis

Fig. 1. Bolbosoma nipponicum collected from Callorhinus ursinus (Linnaeus) (Carnivora: Otariidae) in St. Paul Island, Alaska. A: female; B: hooks; C: proboscis; D: male; E: trunk spines; F: testes and cement-glands; G: poster part of female. Scale bars: A, D = 1000 μm; B = 100 μm; C = 200 μm; E = 50 μm; F, G = 500 μm.

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Fig. 2 in Molecular phylogeny of the Pseudaliidae (Nematoda) and the origin of associations between lungworms and marine mammals

Fig. 2. Bayesian inference analysis (BI) of the phylogenetic relationships between representatives from all six genera of the Pseudaliidae in relation to the Filaroididae using the concatenated sequences of the cytochrome c oxidase subunit I (cox1) and second internal transcribed spacer (ITS2) DNA regions. Angiostrongylus vasorum (Angiostrongylidae), Metastrongylus salmi (Metastrongylidae), and Crenosoma striatum and Otostrongylus cicumlitus (Crenosomatidae) were used as the outgroups. Nodal support is indicated by BI posterior probabilities; posterior probabilities less than 0.7 are not shown. The scale bar indicates the number of nucleotide substitutions per site. Host key: green, Marine Pseudaliidae; red, Terrestrial Pseudaliidae; blue, Parafilaroides spp.; black, other species of the Metastrongyloidea.

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Fig. 1 in Molecular phylogeny of the Pseudaliidae (Nematoda) and the origin of associations between lungworms and marine mammals

Fig. 1. Maximum-Likelihood (ML) analysis of the phylogenetic relationships between representatives from all six genera of the Pseudaliidae in relation to the Filaroididae using the concatenated sequences of the cytochrome c oxidase subunit I (cox1) and second internal transcribed spacer (ITS2) DNA regions. Angiostrongylus vasorum (Angiostrongylidae), Metastrongylus salmi (Metastrongylidae), and Crenosoma striatum and Otostrongylus cicumlitus (Crenosomatidae) were used as the outgroups. Nodal support is indicated by bootstrap values; bootstrap values less than 70% are not shown. The scale bar indicates the number of nucleotide substitutions per site. Host key: green, Marine Pseudaliidae; red, Terrestrial Pseudaliidae; blue, Parafilaroides spp.; black, other species of the Metastrongyloidea.

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Fig. 3 in Molecular phylogeny of the Pseudaliidae (Nematoda) and the origin of associations between lungworms and marine mammals

Fig. 3. Associations between marine (green branches) and terrestrial (red branch) species of Pseudaliidae, and Parafilaroides (blue branches), mapped onto a partial phylogeny of their Laurasiatheria hosts at familial level. The associations of other species of the Metastrongyloidea for which phylogenetic information exists (see Table 2) are also included. The host phylogeny is based on Burgin et al. (2018), but an alternative hypothesis for the time of splitting between mysticete and odontocete cetaceans (Springer et al., 2019) is also presented (arrow). Abbreviations: Aelur: Aelurostrogylus abstrusus; Angc: Angiocaulus gubernaculatus; Angt1: Angiostrongylus chabaudi; Angt2: Angiostrongylus vasorum; Angt3: Angiostrongylus daskalovi; Creno1: Crenosoma vulpis; Creno2: Crenosoma mephitidis; Elap: Elaphostrongylus alces; Fil: Filaroides martis; Hal: Halocercus spp.; Metast1: Metastrongylus elongatus; Metast2: Metastrongylus pudendotectus, Metast3: Metastrongylus salmi; Mue: Muellerius capillaris; Osl1: Oslerus rostratus; Osl2: Oslerus osleri; Otost: Otostrongylus circumlitus; Par1: Parelaphostrongylus andersoni; Par2: Parelaphostrongylus odocoilei; Par3: Parelaphostrongylus tenuis; Parafil: Parafilaroides spp.; Pero: Perostrongylus falciformis; Ph: Pharurus spp.; Proto1: Protostrongylus rufescens; Proto2: Protostrongylus rupicaprae; Proto3: Protostrongylus shiozawai; Pse: Pseudalius inflexus; Skrj1: Skrjabingylus chitwoodorum; Skrj2: Skrjabingylus santaceciliae; Ste: Stenurus spp.; Stenuroi: Stenuroides herpestis; Tor: Torynurus convolutus; Trilo: Trilobostrongylus bioccai; Trog1: Troglostrongylus brevior; Trog2: Troglostrongylus wilsoni; Umingm; Umingmakstrongylus pallikuukensis; Var: Varestrongylus alpenae.

FIG. 4 in Molecular phylogeny and morphology reveal a new species of genus Rhodocybe sensu stricto Maire (Entolomataceae; Agaricales) from Pakistan

FIG. 4. — Microscopic characters of Rhodocybe pakistanica sp. nov. (LAH37947): A, basidiospores; B, basidia; C, D, cheilo- pleurocystidia; E, gloeoplerous hyphae in hymenial and pileal trama; F, stipitipellis. Scale bars: A, 8 μm; B, C, 10 μm; D, 16 μm; E, 20 μm; F, 25 μm.

FIG. 3 in Molecular phylogeny and morphology reveal a new species of genus Rhodocybe sensu stricto Maire (Entolomataceae; Agaricales) from Pakistan

FIG. 3. — Basidiomata of Rhodocybe pakistanica sp. nov.: A-C, LAH37948; D-F, LAH37947. Scale bars: 15 mm.

FIG. 2 in Molecular phylogeny and morphology reveal a new species of genus Rhodocybe sensu stricto Maire (Entolomataceae; Agaricales) from Pakistan

FIG. 2. — Maximum likelihood phylogenetic tree of sequences of Entolomataceae Kotl. & Pouzar, resulting from the analysis of combined nrITS-28S sequences; maximum likelihood bootstrap BT support values greater than 50% are written above the nodes; new species Rhodocybe pakistanica sp. nov. is indicated in bold font.

FIG. 5 in Molecular phylogeny and morphology reveal a new species of genus Rhodocybe sensu stricto Maire (Entolomataceae; Agaricales) from Pakistan

FIG. 5. — Line drawings of Rhodocybe pakistanica sp. nov. (LAH37947): A, basidiospores; B, basidia; C, cheilo- pleurocystidia;D, gloeoplerous hyphae in hymenial and pileal trama; E, pileipellis; F, stipitipellis. Scale bars: A, 6 μm; B, C, 10 μm; D, 20 μm; E, 12 μm; F, 25 μm.